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Rescooped by Jennifer Mach from Plant Biology Teaching Resources (Higher Education)
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Cell biology of plants, coming of age

Cell biology of plants, coming of age | Emerging Research in Plant Cell Biology | Scoop.it

My passion for cell biology is rooted in my PhD studies at Rockefeller Univesity, one of the great insitutions for the study of cell biology (http://www.rockefeller.edu/about/awards/nobel/). Although Palade, de Duve and Claude were before my time, I learned cell biology from Gunter Blobel, whose research centers on how proteins get to their target destination. As every plant biologist knows, plants offer unique challenges to the study of cell biology. Knowing the positions of proteins in time and space within the cell is just as important as knowing which proteins and mRNAs are in the cell, but not as amenable to high-throughput methods, and especially not in plant cells.

 

Two new papers in Plant Cell advance our understanding of proteins in time and space in plant cells.

 

In "Protein–Protein and Protein–Membrane Associations in the Lignin Pathway", by Bassard et al., analysis of the supramolecular organization of enzymes in the lignin pathway shows that cytochrome P450s oligomerize and move along with the very mobile plant endoplasmic reticulum. Their expression favors relocalization of their soluble partner proteins nearer the membrane and association of sequential enzymes in the pathway. (http://www.plantcell.org/content/early/2012/11/26/tpc.112.102566.full.pdf+html)

 

"The KEEP ON GOING Protein of Arabidopsis Regulates Intracellular Protein Trafficking and Is Degraded during Fungal Infection" by Bu and Innes shows that Arabidopsis KEEP ON GOING plays a central role in regulating movement of proteins from the plasma membrane to the central vacuole and in the secretion of defense proteins to the extracellular space. (http://www.plantcell.org/content/early/2012/11/26/tpc.112.105254.full.pdf+htm).

 

Almost 30 years after my first cell biology course, I still find it mind-boggling how cells manage to move so many proteins, peptides, carbohydrates and other complex molecules in and out and around, using lipid signals, the cytoskeleton, protein complexes, receptors, adaptor proteins etc.- Cells are beautiful!


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Emerging Research in Plant Cell Biology
A science editor's take on what's new and interesting in the plant kingdom.
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Rescooped by Jennifer Mach from Plant roots and rhizosphere
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Cadmium translocation by contractile roots differs from that in regular, non-contractile roots

Cadmium translocation by contractile roots differs from that in regular, non-contractile roots | Emerging Research in Plant Cell Biology | Scoop.it

Background and Aims Contractile roots are known and studied mainly in connection with the process of shrinkage of their basal parts, which acts to pull the shoot of the plant deeper into the ground. Previous studies have shown that the specific structure of these roots results in more intensive water uptake at the base, which is in contrast to regular root types. The purpose of this study was to find out whether the basal parts of contractile roots are also more active in translocation of cadmium to the shoot.

Methods Plants of the South African ornamental species Tritonia gladiolaris were cultivated in vitro for 2 months, at which point they possessed well-developed contractile roots. They were then transferred to Petri dishes with horizontally separated compartments of agar containing 50 µmol Cd(NO3)2 in the region of the root base or the root apex. Seedlings of 4-d-old maize (Zea mays) plants, which do not possess contractile roots, were also transferred to similar Petri dishes. The concentrations of Cd in the leaves of the plants were compared after 10 d of cultivation. Anatomical analyses of Tritonia roots were performed using appropriately stained freehand cross-sections.

Key Results The process of contraction required specific anatomical adaptation of the root base in Tritonia, with less lignified and less suberized tissues in comparison with the subapical part of the root. These unusual developmental characteristics were accompanied by more intensive translocation of Cd ions from the basal part of contractile roots to the leaves than from the apical–subapical root parts. The opposite effects were seen in the non-contractile roots of maize, with higher uptake and transport by the apical parts of the root and lower uptake and transport by the basal part.

Conclusions The specific characteristics of contractile roots may have a significant impact on the uptake of ions, including toxic metals from the soil surface layers. This may be important for plant nutrition, for example in the uptake of nutrients from upper soil layers, which are richer in humus in otherwise nutrient-poor soils, and also has implications for the uptake of surface-soil pollutants.

Background and Aims Contractile roots are known and studied mainly in connection with the process of shrinkage of their basal parts, which acts to pull the shoot of the plant deeper into the ground.

Via Christophe Jacquet
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Rescooped by Jennifer Mach from Plant Biology Teaching Resources (Higher Education)
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A novel highly differentially expressed gene in wheat endosperm associated with bread quality

A novel highly differentially expressed gene in wheat endosperm associated with bread quality | Emerging Research in Plant Cell Biology | Scoop.it

Good one to read with students. The genetics and the plant biology are both easy to understand and the application is very evident.


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Rescooped by Jennifer Mach from Plant-Microbe Symbioses
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Growing rice in controlled environments

Growing rice in controlled environments | Emerging Research in Plant Cell Biology | Scoop.it
Rice (Oryza sativa) is less frequently used in basic research than Arabidopsis, although rice is a valuable model system for many monocot crops and possesses a high genetic variability in physiologically as well as agriculturally relevant features such as abiotic stress tolerance, nutrient efficiency and flower time control. A reason is the seemingly difficult cultivation of rice outside the rice production area. This review aims to assist newcomers to the field to develop cultivation protocols for their local controlled environment. The main challenges are high light demands, photoperiodicity and low micronutrient efficiency. The nutrient efficiency problem can be overcome by adding micronutrient fertiliser to potting substrates and keeping the soil waterlogged to increase micronutrient availability and mobility. Cultivation of rice on adjusted hydroponic solutions with high iron concentration provides the basis for successful heavy isotope labelling. Many rice cultivars need high light intensities in combination with short-day conditions to complete their life cycle. However, some photoperiod-insensitive cultivars will flower even under relatively low light intensities. In highly photoperiod-sensitive cultivars, like Nipponbare, flowering can be induced by a limited period of short-day treatment in the sensitive period, after which the cultivation can be continued in long-day conditions. The life cycle of many cultivars is completed in 90 to 120 days, its length being thus comparable to Arabidopsis and shorter than in other cereals. In conclusion, with the right cultivation technique, rice is an amiable model species for researchers beyond the rice area too.

Via Jean-Michel Ané
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Rescooped by Jennifer Mach from Plant & Evolution
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Genome-wide dosage-dependent and -independent regulation contributes to gene expression and evolutionary novelty in plant polyploids

Polyploidy provides evolutionary and morphological novelties in many plants and some animals. However, the role of genome dosage and composition in gene expression changes remains poorly understood. Here we generated a series of resynthesized Arabidopsis tetraploids that contain 0-4 copies of Arabidopsis thaliana and Arabidopsis arenosagenomes and investigated ploidy and hybridity effects on gene expression. Allelic expression can be defined as dosage–dependent (expression levels correlate with genome dosages) and otherwise dosage–independent. Here we show contribution of many dosage-dependent genes to cell cycle, photosynthesis, and metabolism, whereas dosage-independent genes are enriched in biotic and abiotic stress responses. Interestingly, dosage-dependent genes tend to be preserved in ancient biochemical pathways present in both plant and non-plant species, whereas many dosage-independent genes belong to plant-specific pathways. This is confirmed by an independent analysis using Arabidopsis phylostratigraphic map. ForA. thaliana loci, the dosage-dependent alleles are void of TEs and tend to correlate with H3K9ac, H3K4me3 and CG methylation, whereas the majority of dosage-independent alleles are enriched with TEs and correspond to H3K27me1, H3K27me3 and CHG (H=A, T, or C) methylation. Furthermore, there is a parent-of-origin effect on nonadditively expressed genes in the reciprocal allotetraploids especially when A. arenosa is used as the paternal parent, leading to metabolic and morphological changes. Thus, ploidy, epigenetic modifications, and cytoplasmic-nuclear interactions shape gene expression diversity in polyploids. Dosage-dependent expression can maintain growth and developmental stability, while dosage-independent expression can facilitate functional divergence between homoeologs (subfunctionalization) and/or gain new functions (neofunctionalization) during polyploid evolution.


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Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization

Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization | Emerging Research in Plant Cell Biology | Scoop.it

Autophagy is a primary route for nutrient recycling in plants by which superfluous or damaged cytoplasmic material and organelles are encapsulated and delivered to the vacuole for breakdown. Central to autophagy is a conjugation pathway that attaches AUTOPHAGY-RELATED8 (ATG8) to phosphatidylethanolamine, which then coats emerging autophagic membranes and helps with cargo recruitment, vesicle enclosure, and subsequent vesicle docking with the tonoplast. A key component in ATG8 function is ATG12, which promotes lipidation upon its attachment to ATG5. Here, we fully defined the maize (Zea mays) ATG system transcriptionally and characterized it genetically through atg12 mutants that block ATG8 modification.atg12 plants have compromised autophagic transport as determined by localization of a YFP-ATG8 reporter and its vacuolar cleavage during nitrogen or fixed-carbon starvation. Phenotypic analyses showed that atg12 plants are phenotypically normal and fertile when grown under nutrient-rich conditions. However, when nitrogen-starved, seedling growth is severely arrested, and as the plants mature, they show enhanced leaf senescence and stunted ear development. Nitrogen partitioning studies revealed that remobilization is impaired in atg12plants, which significantly decreases seed yield and nitrogen-harvest index. Together, our studies demonstrate that autophagy, while nonessential, becomes critical during nitrogen stress and severely impacts maize productivity under suboptimal field conditions.

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Enhanced Arabidopsis pattern-triggered immunity by overexpression of cysteine-rich receptor-like kinases

Enhanced Arabidopsis pattern-triggered immunity by overexpression of cysteine-rich receptor-like kinases | Emerging Research in Plant Cell Biology | Scoop.it

Upon recognition of microbe-associated molecular patterns (MAMPs) such as the bacterial flagellin (or the derived peptide flg22) by pattern-recognition receptors (PRRs) such as the FLAGELLIN SENSING2 (FLS2), plants activate the pattern-triggered immunity (PTI) response. The L-type lectin receptor kinase-VI.2 (LecRK-VI.2) is a positive regulator of Arabidopsis thaliana PTI. Cysteine-rich receptor-like kinases (CRKs) possess two copies of the C-X8-C-X2-C (DUF26) motif in their extracellular domains and are thought to be involved in plant stress resistance, but data about CRK functions are scarce. Here, we show that Arabidopsis overexpressing the LecRK-VI.2-responsive CRK4, CRK6, and CRK36 demonstrated an enhanced PTI response and were resistant to virulent bacteria Pseudomonas syringae pv. tomato DC3000. Notably, the flg22-triggered oxidative burst was primed in CRK4, CRK6, and CRK36 transgenics and up-regulation of the PTI-responsive gene FLG22-INDUCED RECEPTOR-LIKE 1 (FRK1) was potentiated upon flg22 treatment in CRK4 and CRK6 overexpression lines or constitutively increased by CRK36overexpression. PTI-mediated callose deposition was not affected by overexpression of CRK4 andCRK6, while CRK36 overexpression lines demonstrated constitutive accumulation of callose. In addition, Pst DC3000-mediated stomatal reopening was blocked in CRK4 and CRK36overexpression lines, while overexpression of CRK6 induced constitutive stomatal closure suggesting a strengthening of stomatal immunity. Finally, bimolecular fluorescence complementation and co-immunoprecipitation analyses in Arabidopsis protoplasts suggested that the plasma membrane localized CRK4, CRK6, and CRK36 associate with the PRR FLS2. Association with FLS2 and the observation that overexpression of CRK4, CRK6, and CRK36 boosts specific PTI outputs and resistance to bacteria suggest a role for these CRKs in Arabidopsis innate immunity.

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Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization

Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization | Emerging Research in Plant Cell Biology | Scoop.it

Autophagy is a primary route for nutrient recycling in plants by which superfluous or damaged cytoplasmic material and organelles are encapsulated and delivered to the vacuole for breakdown. Central to autophagy is a conjugation pathway that attaches AUTOPHAGY-RELATED8 (ATG8) to phosphatidylethanolamine, which then coats emerging autophagic membranes and helps with cargo recruitment, vesicle enclosure, and subsequent vesicle docking with the tonoplast. A key component in ATG8 function is ATG12, which promotes lipidation upon its attachment to ATG5. Here, we fully defined the maize (Zea mays) ATG system transcriptionally and characterized it genetically through atg12 mutants that block ATG8 modification.atg12 plants have compromised autophagic transport as determined by localization of a YFP-ATG8 reporter and its vacuolar cleavage during nitrogen or fixed-carbon starvation. Phenotypic analyses showed that atg12 plants are phenotypically normal and fertile when grown under nutrient-rich conditions. However, when nitrogen-starved, seedling growth is severely arrested, and as the plants mature, they show enhanced leaf senescence and stunted ear development. Nitrogen partitioning studies revealed that remobilization is impaired in atg12plants, which significantly decreases seed yield and nitrogen-harvest index. Together, our studies demonstrate that autophagy, while nonessential, becomes critical during nitrogen stress and severely impacts maize productivity under suboptimal field conditions.

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Rescooped by Jennifer Mach from Plants and Microbes
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Nature Reviews Microbiology: The damage-response framework of microbial pathogenesis (2003)

Nature Reviews Microbiology: The damage-response framework of microbial pathogenesis (2003) | Emerging Research in Plant Cell Biology | Scoop.it

All other curves are derived from this basic curve. The arrow indicates that the position of the curve is variable, and depends on the particular host–microorganism interaction. The y-axis denotes host damage as a function of the host response. In this scheme, host damage can occur throughout the host response, but is magnified at both extremes. The host response is represented by a continuum from 'weak' to 'strong'. 'Weak' and 'strong' are terms that can encompass both quantitative and qualitative characteristics of the host response and are used as the best available terms to denote the spectrum of host response as more precise terms are limiting. Weak responses are those that are insufficient, poor or inappropriate — that is, they are not strong enough to benefit the host. Strong responses are those that are excessive, overly robust or inappropriate — that is, they are too strong and can damage the host. When a threshold amount of damage is reached, the host can become symptomatic and if damage is severe, death can ensue. Green, yellow and purple represent health, disease and severe disease, respectively.


Via Kamoun Lab @ TSL
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Rescooped by Jennifer Mach from Plant & Evolution
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The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops

For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism (SNP) data. While we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased towards non-synonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Lastly, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. While the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.


Via Pierre-Marc Delaux
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Jasmonate signalling in Arabidopsis involves SGT1b–HSP70–HSP90 chaperone complexes

Jasmonate signalling in Arabidopsis involves SGT1b–HSP70–HSP90 chaperone complexes | Emerging Research in Plant Cell Biology | Scoop.it

Plant hormones play pivotal roles in growth, development and stress responses. Although it is essential to our understanding of hormone signalling, how plants maintain a steady state level of hormone receptors is poorly understood. We show that mutation of the Arabidopsis thaliana co-chaperone SGT1b impairs responses to the plant hormones jasmonate, auxin and gibberellic acid, but not brassinolide and abscisic acid, and that SGT1b and its homologue SGT1a are involved in maintaining the steady state levels of the F-box proteins COI1 and TIR1, receptors for jasmonate and auxin, respectively. The association of SGT1b with COI1 is direct and is independent of theArabidopsis SKP1 protein, ASK1. We further show that COI1 is a client protein of SGT1b–HSP70–HSP90 chaperone complexes and that the complexes function in hormone signalling by stabilizing the COI1 protein. This study extends the SGT1b–HSP90 client protein list and broadens the functional scope of SGT1b–HSP70–HSP90 chaperone complexes.

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Molecular principles of membrane microdomain targeting in plants: Trends in Plant Science

Molecular principles of membrane microdomain targeting in plants: Trends in Plant Science | Emerging Research in Plant Cell Biology | Scoop.it
•Proteins and lipids segregate into distinct and coexisting membrane microdomains in vivo.•New microscopy techniques will facilitate the visualization of membrane microdomains and protein dynamics in vivo.•Protein targeting to specific sites in the PM is dynamic and a consequence of combinatorial events.•The cell wall–PM–cytoskeleton continuum is a hallmark of membrane microdomain assembly in plants.

 

Plasma membranes (PMs) are heterogeneous lipid bilayers comprising diverse subdomains. These sites can be labeled by various proteins in vivo and may serve as hotspots for signal transduction. They are found at apical, basal, and lateral membranes of polarized cells, at cell equatorial planes, or almost isotropically distributed throughout the PM. Recent advances in imaging technologies and understanding of mechanisms that allow proteins to target specific sites in PMs have provided insights into the dynamics and complexity of their specific segregation. Here we present a comprehensive overview of the different types of membrane microdomain and describe the molecular modes that determine site-directed targeting of membrane-resident proteins at the PM.

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Rescooped by Jennifer Mach from Plants and Microbes
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Molecular Plant Pathology: A new look at plant viruses and their potential beneficial roles in crops (2015)

Molecular Plant Pathology: A new look at plant viruses and their potential beneficial roles in crops (2015) | Emerging Research in Plant Cell Biology | Scoop.it

Twenty years ago most people (including many scientists) thought of bacteria solely as agents of disease, best treated with disinfectants and antibiotics. Today, most of us are aware that bacteria make up almost 90% of the cells in our bodies, and play a critical role in digestion and the immune response. In plants, bacteria also form important mutualistic relationships, providing nitrogen fixation, growth enhancement and defence against pathogens, and undoubtedly a host of other functions that have yet to be described. The stigma of bacteria has changed dramatically in recent decades, and most people are aware that we need our good microbes.

 

Although there have been recent efforts to characterize the plant microbiome with a focus on finding beneficial microbes, viruses generally have not been included in the beneficial microbe lists (Berg et al., 2014, and references cited therein). Recent work has indicated that they can also play important and beneficial roles in plants, especially in extreme environments in which they are involved in conferring tolerance to drought, cold and hot soil temperatures (Roossinck, 2011). Beneficial viruses are defined for the purposes of this discussion as viruses that provide a trait to crop plants that increases their value or growth potential, or decreases the need for the use of chemical fertilizers or pesticides.

 

See also http://www.noble.org/ag/research/microbes/


Via Kamoun Lab @ TSL
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Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana | Emerging Research in Plant Cell Biology | Scoop.it

Soil water availability represents one of the most important selective agents for plants in nature and the single greatest abiotic determinant of agricultural productivity, yet the genetic bases of drought acclimation responses remain poorly understood. Here, we developed a systems-genetic approach to characterize quantitative trait loci (QTLs), physiological traits and genes that affect responses to soil moisture deficit in the TSUxKAS mapping population of Arabidopsis thaliana. To determine the effects of candidate genes underlying QTLs, we analyzed gene expression as a covariate within the QTL model in an effort to mechanistically link markers, RNA expression, and the phenotype. This strategy produced ranked lists of candidate genes for several drought-associated traits, including water use efficiency, growth, abscisic acid concentration (ABA), and proline concentration. As a proof of concept, we recovered known causal loci for several QTLs. For other traits, including ABA, we identified novel loci not previously associated with drought. Furthermore, we documented natural variation at two key steps in proline metabolism and demonstrated that the mitochondrial genome differentially affects genomic QTLs to influence proline accumulation. These findings demonstrate that linking genome, transcriptome, and phenotype data holds great promise to extend the utility of genetic mapping, even when QTL effects are modest or complex.

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A cascade of arabinosyltransferases controls shoot meristem size in tomato

A cascade of arabinosyltransferases controls shoot meristem size in tomato | Emerging Research in Plant Cell Biology | Scoop.it

Shoot meristems of plants are composed of stem cells that are continuously replenished through a classical feedback circuit involving the homeobox WUSCHEL (WUS) gene and the CLAVATA(CLV) gene signaling pathway. In CLV signaling, the CLV1 receptor complex is bound by CLV3, a secreted peptide modified with sugars. However, the pathway responsible for modifying CLV3 and its relevance for CLV signaling are unknown. Here we show that tomato inflorescence branching mutants with extra flower and fruit organs due to enlarged meristems are defective in arabinosyltransferase genes. The most extreme mutant is disrupted in a hydroxyproline O-arabinosyltransferase and can be rescued with arabinosylated CLV3. Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. Finally, we show that a mutation in CLV3increased fruit size during domestication. Our findings uncover a new layer of complexity in the control of plant stem cell proliferation.

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A Developmental Framework for Graft Formation and Vascular Reconnection in Arabidopsis thaliana: Current Biology

Plant grafting is a biologically important phenomenon involving the physical joining of two plants to generate a chimeric organism. It is widely practiced in horticulture and used in science to study the long-distance movement of molecules. Despite its widespread use, the mechanism of graft formation and vascular reconnection is not well understood. Here, we study the dynamics and mechanisms of vascular regeneration in Arabidopsis thaliana during graft formation when the vascular strands are severed and reconnected. We demonstrate a temporal separation between tissue attachment, phloem connection, root growth, and xylem connection. By analyzing cell division patterns and hormone responses at the graft junction, we found that tissues initially show an asymmetry in cell division, cell differentiation, and gene expression and, through contact with the opposing tissue, lose this asymmetry and reform the vascular connection. In addition, we identified genes involved in vascular reconnection at the graft junction and demonstrate that these auxin response genes are required below the graft junction. We propose an inter-tissue communication process that occurs at the graft junction and promotes vascular connection by tissue-specific auxin responses involvingABERRANT LATERAL ROOT FORMATION 4 (ALF4). Our study has implications for phenomena where forming vascular connections are important including graft formation, parasitic plant infection, and wound healing.

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Traffic Lines: New Tools for Genetic Analysis in Arabidopsis thaliana

Genetic analysis requires the ability to identify the genotypes of individuals in a segregating population. This task is straightforward if each genotype has a distinctive phenotype, but is difficult if these genotypes are phenotypically similar or identical. We show that Arabidopsisseeds homozygous or heterozygous for a mutation of interest can be identified in a segregating family by placing the mutation in trans to a chromosome carrying a pair of seed-expressed green and red fluorescent transgenes (a “traffic line”) that flank the mutation. Nonfluorescent seeds in the self-pollinated progeny of such a heterozygous plant are usually homozygous for the mutation, whereas seeds with intermediate green and red fluorescence are typically heterozygous for the mutation. This makes it possible to identify seedlings homozygous for mutations that lack an obvious seedling phenotype, and also facilitates the analysis of lethal or sterile mutations, which must be propagated in heterozygous condition. Traffic lines can also be used to identify progeny that have undergone recombination within a defined region of the genome, facilitating genetic mapping and the production of near-isogenic lines. We produced 488 transgenic lines containing single genome-mapped insertions of NAP:dsRED and NAP:eGFP in Columbia (330 lines) and Landsberg erecta (158 lines) and generated sets of traffic lines that span most regions of the Arabidopsis genome. We demonstrated the utility of these lines for identifying seeds of a specific genotype and for generating near-isogenic lines using mutations of WUSCHEL and SHOOTMERISTEMLESS. This new resource significantly decreases the effort and cost of genotyping segregating families and increases the efficiency of experiments that rely on the ability to detect recombination in a defined chromosomal segment.

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Diversification of histone H2A variants during plant evolution

Among eukaryotes, the four core histones show an extremely high conservation of their structure and form nucleosomes that compact, protect, and regulate access to genetic information. Nevertheless, in multicellular eukaryotes the two families, histone H2A and histone H3, have diversified significantly in key residues. We present a phylogenetic analysis across the green plant lineage that reveals an early diversification of the H2A family in unicellular green algae and remarkable expansions of H2A variants in flowering plants. We define motifs and domains that differentiate plant H2A proteins into distinct variant classes. In non-flowering land plants, we identify a new class of H2A variants and propose their possible role in the emergence of the H2A.W variant class in flowering plants.


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Natural Variation Identifies ICARUS1 , a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana

Natural Variation Identifies  ICARUS1 , a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in  Arabidopsis thaliana | Emerging Research in Plant Cell Biology | Scoop.it

Plants are highly sensitive to environmental changes and even small variations in ambient temperature have severe consequences on their growth and development. Temperature affects multiple aspects of plant development, but the processes and mechanisms underlying thermo-sensitive growth responses are mostly unknown. Here we exploit natural variation inArabidopsis thaliana to identify and characterize novel components and processes mediating thermo-sensitive growth responses in plants. Phenotypic screening of wild accessions identified several strains displaying pleiotropic growth defects, at cellular and organism levels, specifically at high ambient temperatures. Positional cloning and characterization of the underlying gene revealed that ICARUS1 (ICA1), which encodes a protein of the tRNAHis guanylyl transferase (Thg1) superfamily, is required for plant growth at high temperatures. Transcriptome and gene marker analyses together with DNA content measurements show that ICA1 loss-of-function results in down regulation of cell cycle associated genes at high temperatures, which is linked with a block in G2/M transition and endoreduplication. In addition, plants with mutations in ICA1show enhanced sensitivity to DNA damage. Characterization of additional strains that carry lesions in ICA1, but display normal growth, shows that alternative splicing is likely to alleviate the deleterious effects of some natural mutations. Furthermore, analyses of worldwide and regional collections of natural accessions indicate that ICA1 loss-of-function has arisen several times independently, and that these occur at high frequency in some local populations. Overall our results suggest that ICA1-mediated-modulation of fundamental processes such as tRNAHismaturation, modify plant growth responses to temperature changes in a quantitative and reversible manner, in natural populations.

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The Plant Journal - Volume 82, Issue 3 - Chlamydomonas

The Plant Journal - Volume 82, Issue 3 - Chlamydomonas | Emerging Research in Plant Cell Biology | Scoop.it

Special issue on Chlamydomonas-- all open access!

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Plant J: Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions (2012)

Plant J: Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions (2012) | Emerging Research in Plant Cell Biology | Scoop.it

Attack and counter-attack impose strong reciprocal selection on pathogens and hosts, leading to development of arms race evolutionary dynamics. Here we show that Magnaporthe oryzae avirulence gene AVR-Pik and the cognate rice resistance (R) gene Pik are highly variable, with multiple alleles in which DNA replacements cause amino acid changes. There is tight recognition specificity of the AVR-Pikalleles by the various Pik alleles. We found that AVR-Pik physically binds the N-terminal coiled-coil domain of Pik in a yeast two-hybrid assay as well as in an in planta co-immunoprecipitation assay. This binding specificity correlates with the recognition specificity between AVR and R genes. We propose that AVR-Pik and Pik are locked into arms race co-evolution driven by their direct physical interactions.


Via Kamoun Lab @ TSL
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The origins of reproductive isolation in plants

The origins of reproductive isolation in plants | Emerging Research in Plant Cell Biology | Scoop.it

Reproductive isolation in plants occurs through multiple barriers that restrict gene flow between populations, but their origins remain uncertain. Work in the past decade has shown that postpollination barriers, such as the failure to form hybrid seeds or sterility of hybrid offspring, are often less strong than prepollination barriers. Evidence implicates multiple evolutionary forces in the origins of reproductive barriers, including mutation, stochastic processes and natural selection. Although adaptation to different environments is a common element of reproductive isolation, genomic conflicts also play a role, including female meiotic drive. The genetic basis of some reproductive barriers, particularly flower colour influencing pollinator behaviour, is well understood in some species, but the genetic changes underlying many other barriers, especially pollen–stylar interactions, are largely unknown. Postpollination barriers appear to accumulate at a faster rate in annuals compared with perennials, due in part to chromosomal rearrangements. Chromosomal changes can be important isolating barriers in themselves but may also reduce the recombination of genes contributing to isolation. Important questions for the next decade include identifying the evolutionary forces responsible for chromosomal rearrangements, determining how often prezygotic barriers arise due to selection against hybrids, and establishing the relative importance of genomic conflicts in speciation.


Via Pierre-Marc Delaux
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The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice

Non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. A targeted search for jasmonate-induced metabolites in cultivated rice (Oryza sativa) identified (R)-β-tyrosine, an isomer of the common amino acid (S)-α-tyrosine in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temperate japonica cultivars. Genetic mapping identified a candidate gene on chromosome 12, which was confirmed to encode a tyrosine aminomutase (TAM1) by transient expression in Nicotiana benthamiana and in vitro enzyme assays. A point mutation in TAM1 eliminated β-tyrosine production in Nipponbare. Rice cultivars that do not produce β-tyrosine have a chromosome 12 deletion that encompasses TAM1. Although β-tyrosine accumulation was induced by the plant defense signaling molecule jasmonic acid, bioassays with hemipteran and lepidopteran herbivores showed no negative effects at physiologically relevant β-tyrosine concentrations. In contrast, root growth ofArabidopsis thaliana and other tested dicot plants was inhibited by concentrations as low as 1 μM. As β-tyrosine is exuded into hydroponic medium at higher concentrations, it may contribute to the allelopathic potential of rice.

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Featured in an In Brief by yours truly:

http://www.plantcell.org/content/early/2015/04/21/tpc.15.00312

 

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A robustCRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicotplants: Molecular Plant

CRISPR/Cas9 targeting systems have been applied to a variety of species. However, most of current CRISPR/Cas9 systems for plantscan only modify one or a few target sites. Here, we report a robust CRISPR/Cas9 vector system, utilizing a plant codon-optimized Cas9 gene, for convenient and high-efficiency multiplex genome editing in monocot and dicot plants.We designed PCR-based procedures to rapidly generate multiple sgRNA expression cassettes, which can be assembled into the binary CRISPR/Cas9 vectors in one round of cloning by Golden Gate ligation or Gibson Assembly. With this system, we edited 46target sites in rice with average 85.4% of mutation rate, mostly in biallelic and homozygous statuses. We reasoned that about 16% of the homozygous mutations in rice were generated through the nonhomologous end joining mechanism followed by homologous recombination-based repairing. We also obtained uniform biallelic, heterozygous, homozygous, and chimeric mutations in ArabidopsisT1 plants. Thetargeted mutations in both rice and Arabidopsiswereheritable.We provide examples of loss-of-function gene mutations in T0 rice and T1Arabidopsis plants by simultaneous targeting of multiple (up to 8) membersof a gene family, multiple genes in a biosynthetic pathway, or multiple sites in a single gene.This systemhas provided a versatile toolbox for studying functions of multiple genes and gene families in plants for basic research and genetic improvement.

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What Do You Mean, “Epigenetic”?

Interest in the field of epigenetics has increased rapidly over the last decade, with the term becoming more identifiable in biomedical research, scientific fields outside of the molecular sciences, such as ecology and physiology, and even mainstream culture. It has become increasingly clear, however, that different investigators ascribe different definitions to the term. Some employ epigenetics to explain changes in gene expression, others use it to refer to transgenerational effects and/or inherited expression states. This disagreement on a clear definition has made communication difficult, synthesis of epigenetic research across fields nearly impossible, and has in many ways biased methodologies and interpretations. This article discusses the history behind the multitude of definitions that have been employed since the conception of epigenetics, analyzes the components of these definitions, and offers solutions for clarifying the field and mitigating the problems that have arisen due to these definitional ambiguities.

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